How do I reprogram the Linux boot partitions in the micro SD Flash card from JTAG?

[Altera_Forum]

Hi, 

 We are working with a number of Arria V SoC development boards remotely. We have an attached Linux PC with access to user accounts, Altera design software and USB connections to the Console and to the JTAG port. So we can reprogram the FPGA fabric and login to the Linux Console. The problem is if we mess up the remote programming of the boot partitions we are locked out of the Linux interface. We can still reprogam the FPGA fabric but not the Linux boot partitions. It seems there should be a way through JTAG to remotely reprogam the boot parttions in the micro SD flash card. How do we do that?   Thanks Martin

[Altera_Forum]

So I am thinking I probably cannot program the SD card flash from the JTAG interface, but I can program the SPI attached flash. So is it possible to configure a flash image file which includes FPGA config and the 3 Linux boot partitions and program that via JTAG to the SPI attached flash and then configure the Linux system to boot from the SPI flash? 

 Thanks Martin